void load_annot(const boost::filesystem::path file_path, int start_index, int end_index);
//! load sequence annotations
//! \throws mussa_load_error
- void load_annot(std::fstream& data_stream, int start_index, int end_index);
+ void load_annot(std::istream& data_stream, int start_index, int end_index);
//! parse annotation file
/*! \throws annotation_load_error
*/
//! create an initialized annotation with the "standard" types.
SeqSpanRef make_annotation(std::string name, std::string type, size_type start, size_type stop) const;
const SeqSpanRefList& annotations() const;
+
const MotifList& motifs() const;
//! add a motif to our list of motifs
//! annotate the current sequence with other sequences
void find_sequences(std::list<Sequence>::iterator start,
std::list<Sequence>::iterator end);
+ SeqSpanRef seqspan() { return seq; }
void save(boost::filesystem::fstream &save_file);
- void load_museq(boost::filesystem::path load_file_path, int seq_num);
+ //void load_museq(boost::filesystem::path load_file_path, int seq_num);
+ static SequenceRef load_museq(boost::filesystem::fstream& load_file);
protected:
SeqSpanRef seq;